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At least 1,261 records · Page 70Linked to original sources

Effect of retinoic acid on gene expression in human conjunctival epithelium: secretory phospholipase A2 mediates retinoic acid induction of MUC16.

PURPOSE: How vitamin A contributes to the maintenance of the wet-surfaced phenotype at the ocular surface is not well understood. This study sought to identify vitamin A-responsive genes in ocular surface epithelia using gene microarray analysis of cultures of a human conjunctival epithelial (HCjE) cell line grown with all-trans-retinoic acid (RA). The analysis showed that secretory phospholipase A(2) group IIA (sPLA(2)-IIA) was the gene most upregulated by RA, followed by the membrane-associated mucin MUC16 at a later time point. Since eicosanoids, the product of arachidonic acid generated by the PLA(2) family, have been shown to increase mucin production, this study sought to determine whether sPLA(2) mediates the RA induction of MUC16. METHODS: HCjE cells were cultured with or without RA for 3, 6, 24, and 48 hours. Complementary RNA prepared from RNA of the HCjE cells was hybridized to human gene chips and analyzed using commercial software. Microarray data on mucin expression were validated by real-time PCR. To investigate whether sPLA(2) is associated with RA-induced MUC16 upregulation, HCjE cells were incubated with RA and the broad-spectrum PLA(2) inhibitor aristolochic acid (ArA) or the specific sPLA(2)-IIA inhibitor LY315920, followed by analysis of MUC16 mRNA and protein by real-time PCR and Western blot analysis. RESULTS: After RA addition, 28 transcripts were upregulated and 6 downregulated by more than twofold (P < 0.01) at both 3 and 6 hours (early phase). Eighty gene transcripts were upregulated and 45 downregulated at both 24 and 48 hours (late phase). Group IIA sPLA(2), significantly upregulated by 24 hours, and MUC16 were the most upregulated RNAs by RA at 48 hours. sPLA(2) upregulation by RA was confirmed by Western blot analysis. When HCjE cells were incubated with RA plus ArA or specific inhibitor of sPLA(2)-IIA, LY315920, the RA-induced MUC16 mRNA was significantly reduced (P < 0.01). CONCLUSIONS: The RA-associated upregulation of membrane-associated mucin MUC16 at late phase appears to be through sPLA(2)-IIA. Upregulation of this hydrophilic membrane-associated mucin may be one of the important mechanisms by which vitamin A facilitates maintenance of the wet-surfaced phenotype on the ocular surface.

Acetates↗

Multiple sclerosis medical image analysis and information management.

Magnetic resonance imaging (MRI) has become a central tool for patient management, as well as research, in multiple sclerosis (MS). Measurements of disease burden and activity derived from MRI through quantitative image analysis techniques are increasingly being used. There are many complexities and challenges in building computerized processing pipelines to ensure efficiency, reproducibility, and quality control for MRI scans from MS patients. Such paradigms require advanced image processing and analysis technologies, as well as integrated database management systems to ensure the most utility for clinical and research purposes. This article reviews pipelines available for quantitative clinical MRI research in MS, including image segmentation, registration, time-series analysis, performance validation, visualization techniques, and advanced medical imaging software packages. To address the complex demands of the sequential processes, the authors developed a workflow management system that uses a centralized database and distributed computing system for image processing and analysis. The implementation of their system includes a web-form-based Oracle database application for information management and event dispatching, and multiple modules for image processing and analysis. The seamless integration of processing pipelines with the database makes it more efficient for users to navigate complex, multistep analysis protocols, reduces the user's learning curve, reduces the time needed for combining and activating different computing modules, and allows for close monitoring for quality-control purposes. The authors' system can be extended to general applications in clinical trials and to routine processing for image-based clinical research.

Humans↗

Modelling of Buckingham Canal water quality.

The paper presents a case study of the modelling of the water quality of a canal situated in a petrochemical industrial complex, which receives wastewaters from Madras Refineries Limited (MRL), and Madras Fertilizers Limited (MFL). The canal well known Buckingham Canal which passes through Chennai (Madras), India has been modelled using the software QUAL2E-UNCAS. After testing and validation of the model, simulations have been carried out. The exercise enables forecasting the impacts of different seasons, base flows, and waste water inputs on the water quality of the Buckingham Canal. It also enables development of water management strategies.

Chemical Industry↗

[Extent of agreement in case of complete identity].

Two diagnostic procedures with binary outcomes are usually compared by Cohen's kappa coefficient of agreement. If the results of the two procedures are completely identical on a sample and so kappa equals to 1, the precision of the estimate can not be computed with the usual formulae and statistical softwares. A formula for variance which is valid in this particular case is presented together with a real example.

Analysis of Variance↗

Influence of cyclical mechanical strain on extracellular matrix gene expression in human lamina cribrosa cells in vitro.

PURPOSE: The mechanical effect of raised intraocular pressure is a recognised stimulus for optic neuropathy in primary open angle glaucoma (POAG). Characteristic extracellular matrix (ECM) remodelling accompanies axonal damage in the lamina cribrosa (LC) of the optic nerve head in POAG. Glial cells in the lamina cribrosa may play a role in this process but the precise cellular responses to mechanical forces in this region are unknown. The authors examined global gene expression profiles in lamina cribrosa cells exposed to cyclical mechanical stretch, with an emphasis on ECM genes. METHODS: Glial fibrillary acid protein negative primary LC cells were generated from the optic nerve head tissue of three normal human donors. Confluent cell passages (n=4) were exposed to 15% stretch at 1 Hz or static conditions for 24 h using the Flexercell system. Gene expression was assessed using Affymetrix U133A microarrays with pooled RNA. Expression levels were normalized using robust multi-chip average (RMA). Expression data was annotated using NIH DAVID software. ECM-related gene expression was validated in an independent experiment using quantitative real-time PCR and protein synthesis was measured using ELISA and immunohistochemistry. RESULTS: Compared with static controls, 805 genes were upregulated and 644 were downregulated by +/-1.5 fold in stretched LC cells. Gene ontologies included ECM, cell proliferation, growth factor activity, and signal transduction. Differentially expressed ECM genes included elastin, collagens (IV, VI, VIII, IX), thrombospondin 1, perlecan, and lysl oxidase. Quantitative PCR demonstrated that the expression of TGF-beta2, BMP-7, elastin, collagen VI, biglycan, versican, EMMPRIN, VEGF, and thrombomodulin were reproducible and consistent with the microarray data. VEGF and TGF-beta2 protein levels were also significantly (p<0.05) increased in stretched cell media supernatants. Immunohistochemistry demonstrated increased EMMPRIN (an extracellular matrix metalloproteinase inducer) protein in human POAG optic nerve head tissue compared to nonglaucomatous controls. CONCLUSIONS: These findings demonstrate that LC cells respond to mechanical stimuli in vitro by transcription of several components and modulators of the ECM. Some of the upregulated ECM genes identified are novel in the context of glaucomatous optic neuropathy (biglycan, versican, EMMPRIN, and BMP-7). The LC cell may represent both an important pro-fibrotic cell type in the optic nerve head and an attractive target for novel therapeutic intervention in POAG.

Cells, Cultured↗

Computer-aided analysis of mutagenicity and cell transformation data for assessing their relationship with carcinogenicity.

Using a computer-aided approach, the tests for Salmonella mutagenicity and transformation in established cell lines were compared for the qualitative bases of their carcinogenicity predictions. For this purpose, a database of 145 chemicals was prepared in which rodent carcinogenicity data and results of the Ames' and transformation tests were available. Using a software program for connectivity analysis (previously developed and validated by us), we assayed the molecular structures of these chemicals for the presence of fragments relatable to their positive (i.e., biophores) or negative (i.e., biophobes) response to the tests in question. These fragments were then studied for their association with genotoxic and nongenotoxic carcinogenicity. The philosophy adopted was that the type and number of molecular fragments chosen by the software to describe the chemicals correctly predicted by the tests could be related to the type of carcinogenic effects to which the tests themselves were sensitive. The classifications made by the software were interpreted by human expertise and the biophores found were compared with the acknowledged structural alerts to DNA reactivity as formalized by Ashby and co-workers [(1991): Mutat Res 257:229-306; (1993): Mutat Res 286: 3-74]. The results show that, in quantitative terms, the overall ability to predict carcinogenicity is about the same for both the Salmonella and transformation tests. However, in qualitative terms the transformation test appears to be sensitive to effects that are more heterogeneous than those inducing mutation, some of which are presumably related to nongenotoxic carcinogenic activities. This study illustrates a possible, innovative model of analysis of chemical structures that, using an automated approach along with the biologist's judgment, could contribute to the detection of complementarities among short-term test endpoints.

Animals↗

Automated data processing for chromatographic assay method validations.

A set of computer programs has been developed for the automated transfer, storage, and processing of data related to chromatographic pharmaceutical assay method validations. These programs calculate and report statistical parameters relating to the resolution, linearity of response, and precision of an assay method based upon peak width, retention time, and integration data provided by a commercial chromatographic data system. Utilization of an interface between the data system and a microcomputer minimizes manual handling of all data. Techniques and equations used in the development of the software are described, and an application to the validation of a high performance liquid chromatographic assay method for a bulk drug substance is demonstrated.

Chromatography, High Pressure Liquid↗

An integrated tool for microarray data clustering and cluster validity assessment.

UNLABELLED: In this paper we present a data mining system, which allows the application of different clustering and cluster validity algorithms for DNA microarray data. This tool may improve the quality of the data analysis results, and may support the prediction of the number of relevant clusters in the microarray datasets. This systematic evaluation approach may significantly aid genome expression analyses for knowledge discovery applications. The developed software system may be effectively used for clustering and validating not only DNA microarray expression analysis applications but also other biomedical and physical data with no limitations. AVAILABILITY: The program is freely available for non-profit use on request at http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.html CONTACT: Nadia.Bolshakova@cs.tcd.ie.

Algorithms↗

Risk assessment for HIV infection: validation study of a computer-assisted preliminary screen.

Development has been undertaken for microcomputer software intended to assess individual risk for HIV infection by analyzing personal case histories pertinent to drug abuse, receptive blood transfusion, and sexual behavior. The software performs interactive confidential interviews of individuals desiring expert assistance when deciding whether to commit to an antibody test. In the first phase of a validation study, 87 subjects responded to the computer interview. For each subject, human immunodeficiency virus (HIV) antibody status was on clinical record. This sample included 70 subjects, 29 of whom were HIV seropositive, recruited from the clientele of an AIDS antibody testing and counseling facility. In this phase, the software accurately assessed 28 of 29 seropositives (96.6%) to be at risk for HIV. The second phase was based upon participation of an additional 74 subjects who were undergraduates at the University of Oklahoma. In this presumed low-risk sample, 55 members reported never having previously tested for HIV antibodies. Seven members (12.7%) of the untested group were declared at risk in the course of receiving confidential computer screen advice. Of these 7, there were 3 members (42.9%) who were motivated by the computer to voluntarily seek HIV antibody testing. Of the 7 declared at risk, 2 members (3.9%) were among the 51 seronegative subjects classified as heterosexuals without specific and identified risks. All Phase II subjects seeking follow-up antibody tests were found seronegative.

Diagnosis, Computer-Assisted↗

A new generation patient classification system.

The traditional approaches to monitoring reliability and validity are time consuming and costly and frequently lead to the abandonment of reasonable classification instruments. With the advent of micro computers and relational database software, nursing executives are now able to track reliability and validity on an ongoing basis. Because patient classification data are retained, they can be used to provide more accurate work load predictions and descriptions. Further, the ability to identify the source of problems with unit-specific instruments or nurse classifiers leads to the required corrective mechanism. Increased confidence in the reliability and validity of the work load data provides the staff nurse with direct evidence of the accuracy of the patient classification instrument and the nursing executive with a significantly stronger tool in budget planning and tracking, contract negotiations and financial risk reduction.

Activities of Daily Living↗

Agreement between four available algorithms to evaluate global systolic left and right ventricular function from tomographic radionuclide ventriculography and comparison with planar imaging.

BACKGROUND AND AIM: Left and right ventricular ejection fractions (LVEF and RVEF) and end-diastolic and end-systolic volumes (LVEDV, RVEDV, LVESV and RVESV) can be calculated from tomographic radionuclide ventriculography (TRV). The aim of this study was to validate and compare these parameters obtained using four different TRV software programs (QBS, QUBE, 4D-MSPECT and BP-SPECT). METHODS: LVEF obtained from planar radionuclide ventriculography (PRV) was compared with LVEF obtained from TRV using the four different software programs in 166 patients. Furthermore, ventricular volumes obtained using TRV (QBS, QUBE and 4D-MSPECT) were compared with those obtained using BP-SPECT, the latter being the only method with the validation of ventricular volumes in the literature. RESULTS: The correlation of LVEF between PRV and TRV was good for all methods: 0.81 for QBS, 0.79 for QUBE, 0.71 for 4D-MSPECT and 0.79 for BP-SPECT. The mean differences+/-standard deviation (SD) were 3.16+/-9.88, 10.72+/-10.92, 3.43+/-11.79 and 2.91+/-10.39, respectively. The correlation of RVEF between BP-SPECT and QUBE and QBS was poor: 0.33 and 0.38, respectively. LV volumes calculated using QBS, QUBE and 4D-MSPECT correlated well with those obtained using BP-SPECT (0.98, 0.90 and 0.98, respectively), with mean differences+/-SD of 7.31+/-42.94, -22.09+/-36.07 and -40.55+/-39.36, respectively. RV volumes showed poorer correlation between QBS and BP-SPECT and between QUBE and BP-SPECT (0.82 and 0.57, respectively). CONCLUSION: LVEF calculated using TRV correlates well with that calculated using PRV, but is not interchangeable with the value obtained using PRV. Volume calculations (for left and right ventricle) and RVEF require further validation before they can be used in clinical practice.

Algorithms↗

Initial Experience with an Internally Rotating Transthoracic Three-Dimensional Echocardiographic Probe and Image Acquisition on a Conventional Echocardiogram Machine.

Three-dimensional echocardiography has required motorized external scanning devices that move a standard echo transducer to obtain data sets before reconstruction. These transducer holders are susceptible to axis alignment errors and transducer movement. The use of a three-dimensional workstation makes acquisition cumbersome. An internally rotating 5-MHz "omniplane" transthoracic transducer, specifically designed for three-dimensional echocardiography, and an integrated three-dimensional acquisition software package that allows single machine acquisitions were validated in 50 pediatric patients. Children were 1 day to 16 years old and had 22 different cardiac pathological conditions imaged. Ninety-eight of the 104 (94%) data sets collected were successfully reconstructed in three dimensions. Acquisitions took 3-6 minutes depending on the increment of internal rotation. Minimum total study time to set up and complete the acquisition was 12 minutes. The new probe and software makes three-dimensional acquisitions and reconstructions of consistently high quality, rapid, reliable, and user friendly.

Journal Article↗

[Living conditions of deer in the provinces of Western Pomerania and Lubuskie as revealed by mandibular content of fluoride, calcium and magnesium. II. Detailed statistical analysis with the statistica neural networks software].

Animals from areas contaminated by industrial emissions containing fluoride may accumulate it predominantly in hard tissues. The stable composition of the mandible makes it suitable for the study of accumulation of fluorides and other elements (Mg, Ca). It is also possible to determine the extent of pollution with fluorine compounds around industrial plants and to reveal some of the features of the natural habitat of wild animals. We applied the advanced technique of neural networks to investigate the simultaneous influence of multiple parameters on the accumulation of fluorine, magnesium, and calcium in the mandible of deer and possible interactions between these elements. The first step involved the generation of a neural network. In the present work, networks were created with the Intelligent Problem Solver (IPS). Input data were divided into three sets. One was used for training (Tr) of the network, another for validation (Ve) and control over the training process and the last one for testing (Te). Network quality was checked with the following parameters: Data Mean--average value of variable; Data SD--standard deviation of variable; Error Mean--average value of error; Abs. Mean--average error modulus; Error SD--standard deviation of error; SD Ratio--ratio of standard deviation of error to standard deviation of variable (Error SD/Data SD); Correlation--Pearson's correlation coefficient. For the model to be satisfactory, Pearson's correlation coefficient should be close to 1. In the case of complex problems with an unclear influence of parameters on the process, an analysis of parametric sensitivity must be performed. This task was accomplished automatically with the computer program. It was found that the effect of the same parameters on the accumulation of fluorine, magnesium and calcium varied. The results suggest interactions between the examined elements.

Animals↗

Computerized quality-of-life screening in an oncology clinic.

PURPOSE: The purpose of these studies was to assess the feasibility and reliability of computerized quality-of-life screening for patients attending an outpatient breast cancer clinic. The screening program involved a computerized administration of the European Organization for Research and Treatment of cancer QUality of Life Questionnaire (EORTC QLQ-C30). The computer software generated a screening report that clinic staff members used in the clinical encounter to assist in identifying quality-of-life problems. DESCRIPTION OF STUDY: Two studies are reported. In study I, 36 patients and either their nurses or physicians evaluated the feasibility of the screening program using questionnaires developed for this study. In study II, a separate sample of 50 patients completed both the computerized and paper-and-pencil versions of the QLQ-C30 to assess reliability and consistency of responding. RESULTS: The results of study I indicate that the patients found the computerized administration to be an acceptable means of providing staff members with information on day-to-day functioning. Clinic nurses and physicians indicated that the report was useful in identifying problematic quality-of-life domains. The results of study II indicate that the computerized administration is highly correlated with the paper-and-pencil version and has similar internal consistency. Discrepancies in responses were identified, but were at an acceptable level. CLINICAL IMPLICATIONS: The results of these studies indicate that computerized quality-of-life screening is feasible and may provide reliable data for research and quality assurance studies. Staff evaluations suggest that the written report may provide clinic staff members with a tool for identifying quality-of-life concerns in which individual patients are experiencing difficulty. Potential benefit to patients include productive use of waiting room time, greater efficiency in the assessment process, and an improved likelihood that nurses and physicians will recognize and attend to quality-of-life deficits. The valid, reliable, and efficient identification of important patient quality-of-life concerns allows multidisciplinary team members to focus meaningfully their clinical efforts within their respective areas of responsibility.

Adult↗

Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studies.

We report the development and validation of experimental methods, study designs, and analysis software for pooling-based genomewide association (GWA) studies that use high-throughput single-nucleotide-polymorphism (SNP) genotyping microarrays. We first describe a theoretical framework for establishing the effectiveness of pooling genomic DNA as a low-cost alternative to individually genotyping thousands of samples on high-density SNP microarrays. Next, we describe software called "GenePool," which directly analyzes SNP microarray probe intensity data and ranks SNPs by increased likelihood of being genetically associated with a trait or disorder. Finally, we apply these methods to experimental case-control data and demonstrate successful identification of published genetic susceptibility loci for a rare monogenic disease (sudden infant death with dysgenesis of the testes syndrome), a rare complex disease (progressive supranuclear palsy), and a common complex disease (Alzheimer disease) across multiple SNP genotyping platforms. On the basis of these theoretical calculations and their experimental validation, our results suggest that pooling-based GWA studies are a logical first step for determining whether major genetic associations exist in diseases with high heritability.

Alzheimer Disease↗

Record linkage of health care insurance claims.

OBJECTIVE: This paper provides a detailed description of a method developed for purposes of linking records of individual patients, represented in diverse data sets, across time and geography. DESIGN: The procedure for record linkage has three major components-data standardization, weight estimation, and matching. The proposed method was designed to incorporate a combination of exact and probabilistic matching techniques. MEASUREMENTS: The procedure was validated using convergent, divergent, and criterion validity measures. RESULTS: The output of the process achieved a sensitivity of 92 percent and a specificity that approached 100 percent. CONCLUSIONS: The procedure is a first step in addressing the current trend toward larger and more complex databases.

Humans↗

A general method for bead-enhanced quantitation by flow cytometry.

Flow cytometry provides accurate relative cellular quantitation (percent abundance) of cells from diverse samples, but technical limitations of most flow cytometers preclude accurate absolute quantitation. Several quantitation standards are now commercially available which, when added to samples, permit absolute quantitation of CD4+ T cells. However, these reagents are limited by their cost, technical complexity, requirement for additional software and/or limited applicability. Moreover, few studies have validated the use of such reagents in complex biological samples, especially for quantitation of non-T cells. Here we show that addition to samples of known quantities of polystyrene fluorescence standardization beads permits accurate quantitation of CD4+ T cells from complex cell samples. This procedure, here termed single bead-enhanced cytofluorimetry (SBEC), was equally capable of enumerating eosinophils as well as subcellular fragments of apoptotic cells, moieties with very different optical and fluorescent characteristics. Relative to other proprietary products, SBEC is simple, inexpensive and requires no special software, suggesting that the method is suitable for the routine quantitation of most cells and other particles by flow cytometry.

Adoptive Transfer↗

A neural network model approach to the study of human TAP transporter.

We used an artificial neural network (ANN) computer model to study peptide binding to the human transporter associated with antigen processing (TAP). After validation, an ANN model of TAP-peptide binding was used to mine a database of HLA-binding peptides to elucidate patterns of TAP binding. The affinity of HLA-binding peptides for TAP was found to differ according to the HLA supertype concerned: HLA-B27, -A3 or -A24 binding peptides had high, whereas HLA-A2, -B7 or -B8 binding peptides had low affinity for TAP. These results support the idea that TAP and particular HLA molecules may have co-evolved for efficient peptide processing and presentation. The strong similarity between the sets of peptides bound by TAP or HLA-B27 suggests functional co-evolution whereas the lack of a relationship between the sets of peptides bound by TAP or HLA-A2 is against these particular molecules having co-evolved. In support of these conclusions, the affinities of HLA-A2 and HLA-B7 binding peptides for TAP show similar distributions to that of randomly generated peptides. On the basis of these results we propose that HLA alleles constitute two separate classes: those that are TAP-efficient for peptide loading (HLA-B27, -A3 and -A24) and those that are TAP-inefficient (HLA-A2, -B7 and -B8). Computer modelling can be used to complement laboratory experiments and thereby speed up knowledge discovery in biology. In particular, we provide evidence that large-scale experiments can be avoided by combining initial experimental data with limited laboratory experiments sufficient to develop and validate appropriate computer models. These models can then be used to perform large-scale simulated experiments the results of which can then be validated by further small-scale laboratory experiments.

ATP Binding Cassette Transporter, Subfamily B, Mem↗